GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garL in Burkholderia phytofirmans PsJN

Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate BPHYT_RS28905 BPHYT_RS28905 alpha-dehydro-beta-deoxy-D-glucarate aldolase

Query= SwissProt::P23522
         (256 letters)



>FitnessBrowser__BFirm:BPHYT_RS28905
          Length = 267

 Score =  231 bits (588), Expect = 2e-65
 Identities = 121/250 (48%), Positives = 167/250 (66%), Gaps = 1/250 (0%)

Query: 8   NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG 67
           N FK ALA  + Q G W+AL++   TE+L  AGFDWL++D EHAPND+ + + QL A+  
Sbjct: 6   NNFKRALAEGKPQFGLWAALADAYVTELLATAGFDWLLIDNEHAPNDVRSTLAQLQAVAA 65

Query: 68  SASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGV-SVS 126
            AS PVVR   ++  +IK+LLDIG    L+P ++T E+A  AVA+TRYPP+GIRGV S  
Sbjct: 66  YASHPVVRPVRSDSALIKQLLDIGAQTLLLPMIDTAEQAADAVAATRYPPQGIRGVGSAL 125

Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186
            RA+ +  + DY   +   + +LVQ+ES QG++N+ AIAA +GVDG+F GPSDL+A++G 
Sbjct: 126 ARASRWNRIPDYLNTAADELCVLVQVESVQGMENLSAIAAVDGVDGVFFGPSDLSASMGL 185

Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSA 246
           LG      V++AI++        GK +G+LAP  A A  YLE GATFVAVG+D G+   A
Sbjct: 186 LGKPGDASVREAIRNGIQTVLRAGKAAGVLAPDPAIAADYLEAGATFVAVGTDTGLLSRA 245

Query: 247 TQKLADTFKK 256
              LA ++KK
Sbjct: 246 AADLAASYKK 255


Lambda     K      H
   0.318    0.134    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 215
Number of extensions: 8
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 256
Length of database: 267
Length adjustment: 25
Effective length of query: 231
Effective length of database: 242
Effective search space:    55902
Effective search space used:    55902
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory